Dear.
I had a MR image like this.
[root@kphe 0534]# avwhd 0534
filename 0534
sizeof_hdr 348
data_type
db_name
extents 0
session_error 0
regular r
hkey_un0
dim0 3
dim1 238
dim2 256
dim3 256
dim4 1
dim5 1
dim6 1
dim7 1
vox_units
cal_units
unused1 0
datatype 4
bitpix 16
pixdim0 0.0000000000
pixdim1 256.0000000000
pixdim2 256.0000000000
pixdim3 256.0000000000
pixdim4 0.0000000000
pixdim5 1.0000000000
pixdim6 1.0000000000
pixdim7 1.0000000000
vox_offset 0.0000
funused1 1.0000
funused2 0.0000
funused3 0.0000
cal_max 0.0000
cal_min 0.0000
compressed 0
verified 0
glmax 0
glmin 0
descrip FSL3.2beta
aux_file
orient 0
originator
origin1 0
origin2 0
origin3 0
generated
scannum
patient_id
exp_date
exp_time
hist_un0
views 0
vols_added 0
start_field 0
field_skip 0
omax 0
omin 0
smin 0
smin 0
file_type ANALYZE-7.5
file_code 0
Because this image contain large amount of neck. I select the part of the
image using avwroi. Results were fine. Header information is as below.
[root@kphe 0534]# avwhd t1
filename t1.nii.gz
sizeof_hdr 348
data_type INT16
dim0 3
dim1 237
dim2 255
dim3 214
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 4
nbyper 2
bitpix 16
pixdim0 0.0000000000
pixdim1 256.0000000000
pixdim2 256.0000000000
pixdim3 256.0000000000
pixdim4 1.0000000000
pixdim5 1.0000000000
pixdim6 1.0000000000
pixdim7 1.0000000000
vox_offset 352
cal_max 0.0000
cal_min 0.0000
scl_slope 0.000000
scl_inter 0.000000
phase_dim 0
freq_dim 0
slice_dim 0
slice_name Unknown
slice_code 0
slice_start 0
slice_end 0
slice_duration 0.000000
time_offset 0.000000
intent Unknown
intent_code 0
intent_name
intent_p1 0.000000
intent_p2 0.000000
intent_p3 0.000000
qform_name Unknown
qform_code 0
qto_xyz:1 256.000000 0.000000 0.000000 0.000000
qto_xyz:2 0.000000 256.000000 0.000000 0.000000
qto_xyz:3 0.000000 0.000000 256.000000 0.000000
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Left-to-Right
qform_yorient Posterior-to-Anterior
qform_zorient Inferior-to-Superior
sform_name Unknown
sform_code 0
sto_xyz:1 0.000000 0.000000 0.000000 0.000000
sto_xyz:2 0.000000 0.000000 0.000000 0.000000
sto_xyz:3 0.000000 0.000000 0.000000 0.000000
sto_xyz:4 0.000000 0.000000 0.000000 0.000000
sform_xorient Unknown
sform_yorient Unknown
sform_zorient Unknown
file_type NIFTI-1+
file_code 1
descrip FSL3.2beta
aux_file
Then, I want to resample using ApplyXFM. Result file is like this.
[root@kphe 0534]# avwhd t1r
filename t1r.nii.gz
sizeof_hdr 348
data_type INT16
dim0 3
dim1 256
dim2 256
dim3 110
dim4 1
dim5 1
dim6 1
dim7 1
vox_units mm
time_units s
datatype 4
nbyper 2
bitpix 16
pixdim0 0.0000000000
pixdim1 0.9375000000
pixdim2 0.9375000000
pixdim3 1.5000000000
pixdim4 1.0000000000
pixdim5 1.0000000000
pixdim6 1.0000000000
pixdim7 1.0000000000
vox_offset 352
cal_max 0.0000
cal_min 0.0000
scl_slope 0.000000
scl_inter 0.000000
phase_dim 0
freq_dim 0
slice_dim 0
slice_name Unknown
slice_code 0
slice_start 0
slice_end 0
slice_duration 0.000000
time_offset 0.000000
intent Unknown
intent_code 0
intent_name
intent_p1 0.000000
intent_p2 0.000000
intent_p3 0.000000
qform_name Unknown
qform_code 0
qto_xyz:1 0.937500 0.000000 0.000000 0.000000
qto_xyz:2 0.000000 0.937500 0.000000 0.000000
qto_xyz:3 0.000000 0.000000 1.500000 0.000000
qto_xyz:4 0.000000 0.000000 0.000000 1.000000
qform_xorient Left-to-Right
qform_yorient Posterior-to-Anterior
qform_zorient Inferior-to-Superior
sform_name Unknown
sform_code 0
sto_xyz:1 0.000000 0.000000 0.000000 0.000000
sto_xyz:2 0.000000 0.000000 0.000000 0.000000
sto_xyz:3 0.000000 0.000000 0.000000 0.000000
sto_xyz:4 0.000000 0.000000 0.000000 0.000000
sform_xorient Unknown
sform_yorient Unknown
sform_zorient Unknown
file_type NIFTI-1+
file_code 1
descrip FSL3.2beta
aux_file
But, I can't see the final result image.
When resampling ApplyXFM without avwroi, results were good and image was
visulaized in fslview.
Could you teach me what is the problem?
thanks.
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